Résumé Groundwater is a principal source of water for many semi-arid countries, including Botswana and South Africa. This is especially true for the rural communities within these regions that lie on the periphery of local water scheme pipelines and make direct use of groundwater. The Ramotswa transboundary aquifer, which supplies local communities and nearby cities with fresh groundwater, is a highly productive and unique karst sequence shared by South Africa and Botswana. The objective of the study was to contribute to the available hydrogeological data by means of evaluating groundwater flow, nitrate pollution and the median recession index and master recession curve for the aquifer. The interpreted airborne geophysical data revealed the presence of collapsed features in the northeastern area corresponding to the karst morphology. A piezometric map of the area shows the groundwater flow is towards the north-northeast, which is supported by salinity increase across the study area. Increased nitrate concentrations were identified in areas with increased rainfall, shallow groundwater and a mature karst system. Only 3% of the 36 sample sites had nitrate concentrations exceeding the WHO guideline limit of 50 mg/l. This was attributed to the legacy of unlined pit latrines in karstified areas. Pollution is entirely anthropogenic and generally from non-point sources. A median recession index computed by RECESS program from the Dinokana spring discharge data was 295.7 days per log cycle and the generated master recession curve’s gentle slope alludes to massive storage potential within the karst compartment. The results of the study can alert stakeholders alike of the health risk of direct consumption of the groundwater without pretreatment. Establishing an understanding of the nitrate pollution sources and groundwater flow direction, and estimating the recession index provides informed groundwater pollution and vulnerability management options. This can improve the aquifer resource assessment and the livelihoods of local communities in the face of increasing climate change.